In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.

We analyzed 415 species of birds. All species were divided into 7 groups according to their phenotypic characteristics. Phenotypes were classified in accordance with the Bird of the World research database (https://birdsoftheworld.org, accessed August 20, 2020). Genotypes were analysed as follows. We downloaded complete mitochondrial sequences of birds from Genbank. The sequence of each of the 13 genes was obtained according to the GenBank annotation. Species with duplicated genes were excluded from analysis. Sequences of each gene were aligned independently with MACSE toolkit (Ranwez et al, 2011). Columns of alignment with gaps were excluded by trimAl software (Capella-Gutierrez et al, 2009). Phylogenetic analysis was performed in IQ-Tree 2 package (Minh et al, 2020) based on nucleotide alignment, split into 39 partitions by gene and codon position. As early divergences in the bird tree of life are discordant (Jarvis et al, 2014), we used constraints for bird orders branching in our reconstruction. We applied constraints from the most recent revision of bird phylogeny (Kimball, 2019), which combines nuclear and mitochondrial data to construct a consensus supertree for 707 bird species. Amino acid ancestor states reconstruction was also performed in IQ-Tree with usage of genewise partitioned mtVer evolutionary model.

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